circos.genomicAxis: Add genomic axes

In circlize: Circular Visualization

Add genomic axes

Description

Add genomic axes

Usage

circos.genomicAxis(
    h = "top",
    major.at = NULL,
    labels = NULL,
    major.by = NULL,
    tickLabelsStartFromZero = TRUE,
    labels.cex = 0.4*par("cex"),
    sector.index = get.current.sector.index(),
    track.index = get.current.track.index(),
    ...)

Arguments

h	Position of the axes. "top" or "bottom".
major.at	Major breaks. If major.at is set, major.by is ignored.
labels	labels corresponding to major.at. If labels is set, major.at must be set.
major.by	Increment of major ticks. It is calculated automatically if the value is not set (about every 10 degrees there is a major tick).
tickLabelsStartFromZero	Whether axis tick labels start from 0? This will only affect the axis labels while not affect x-values in cells.
labels.cex	The font size for the axis tick labels.
sector.index	Index for the sector
track.index	Index for the track
...	Other arguments pass to circos.axis.

Details

It assigns proper tick labels under genomic coordinate.

See Also

https://jokergoo.github.io/circlize_book/book/high-level-genomic-functions.html#genomic-axes

Examples

circos.initializeWithIdeogram(chromosome.index = paste0("chr", 1:4), plotType = NULL)
circos.track(ylim = c(0, 1), panel.fun = function(x, y) circos.genomicAxis())
circos.track(ylim = c(0, 1), track.height = 0.1)
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
    circos.genomicAxis(h = "bottom", direction = "inside")
})
circos.clear()

circlize documentation built on May 29, 2024, 1:59 a.m.